Gao, Yiqin

Gao, Yiqin


Institute of Systems and Physical Biology

Senior Principal Investigator

Home page of research group:


  • 2019 - Present

    Shenzhen Bay Laboratory         Senior Principal Investigator

  • 2010 - Present

    Peking University         Professor

  • 2015 - 2019

    Peking University         Dean, College of Chemistry and Molecular Engineering, PKU

  • 2005 - 2010

    Texas A&M University         Assistant Professor

  • 2002 - 2004

    California Institute of Technology & Harvard University         Postdoc

  • 2001

    California Institute of Technology         PhD

Research Areas

Our lab is doing research in the fields of theoretical/computational chemistry and biophysical chemistry. We are developing efficient computational methods and statistical mechanics tools to study the conformations of biological molecules in aqueous solutions, mechanisms of enzymatic reactions, and the solvation effects in chemical reactions. We are also interested in understanding the chromosome folding principle and gene expression regulatory mechanism. The lab is working on the simulation/theoretical studies of the following systems: (1) thermodynamics, dynamics and kinetics of electrolytes solutions (2) dynamics and spectra calculations for aqueous solutions (3) chemical/enzymatic reactions in solutions/at interfaces (4) the modeling of chromatin spatial structures and studying the relations between structures and important genome features (5) multiscale gene regulation mechanism in cell.


Prof. Gao is engaged in basic research in biophysical chemistry and theoretical chemistry, seeking the physical nature and molecular mechanism of complex chemical and biological systems. He has won Distinguished Lectureship Award from the Japanese chemical society in 2014, Promising Scientist Prize in 2014 from Quantum Systems in Chemistry and Physics (QSCP), and Pople Medal from Asia-Pacific Association of Theoretical and Computational Chemistry in 2016.

We focus on developing efficient computational methods and statistical mechanics tools to study complex chemical and biological systems. Prof. Gao has published over 140 papers. Published multiple articles in the following areas:(1) theoretical study of chemical reaction mechanisms in different solution environment, development of theoretical models, and efficient enhanced sampling method. (2)integrative study of three-dimensional structure of chromatin and multiple omics information of genome, transcriptome and epigenome, aiming at a unified understanding of cellular development, differentiation, aging, and pathological processes at the molecular level.


1. Deep representation learning for complex free-energy landscapes


2. The effect of hydration number on the interfacial transport of sodumions


3. Unnatural Cytosine Bases Recognized as Thymines by DNA Polymerases by the Formation of the Watson–Crick Geometry


  • • 2006 Searle Scholar

  • • JST Visiting Scholar, Kobe University, Japan

  • • 2004-2009 Camille and Henry Dreyfus New Faculty Award

  • • Milton and Francis Clauser Prize for the Best Doctoral Thesis, CalTech

  • • Herbert Newby McCoy Award

  • • Li Ming Scholarship, CalTech

  • • Chinese-American Engineers and Scientists Association Scholarship

Selected Publications

1. Zhang J, Lei YK, Yang YI, Gao YQ (2020) Deep learning for variational multiscale molecular modeling. J Chem Phys 153(17):174115. DOI:10.1063/5.0026836

2. Quan H, Yang Y, Liu SR, Tian H, Xue Y, Gao YQ (2020) Chromatin structure changes during various processes from a DNA sequence view. Curr Opin Struc Biol 62:1-8. OI:10.1016/

3. Mondal M, Bhattacharyya D, Gao YQ (2019) Structural properties and influence of solvent on the stability of telomeric four-stranded i-motif DNA. Phys Chem Chem Phys 21(38):21549-21560. DOI:10.1039/c9cp03253c

4. Zhang J, Lei Y-K, Che X, Zhang Z, Yang YI, Gao YQ (2019) Deep Representation Learning for Complex Free-Energy Landscapes. J Phys Chem Lett 10(18):5571-5576. DOI:10.1021/acs.jpclett.9b02012

5. Yang YI, Shao Q, Zhang J, Yang L, Gao YQ (2019) Enhanced sampling in molecular dynamics. J Chem Phys 151(7):070902. DOI:10.1063/1.5109531